I'm pretty sure Dean runs without a lower Z limit switch for similar reasons you have mentioned above. I also ran without limit and Z home switch for a while as I kept getting false e-stops (longest cables, direct into BoB), but my 24V upgrade should sort that out. You'll have to decide what you are comfortable with.

You could locate the 'lower' limit switch right at the top near the stepper motor housing, then connect a long upside-down 'L' shaped bracket to the Z axis so that when it gets near the bottom the bit of the 'L' which sticks out comes down and presses the top of the switch. This might look a bit untidy but its an option and is well out of the way of the swarf.

If you've been following the recent build logs you'll see some useful circuit diagrams for wiring limits etc. which avoids the problem you mention above. Once you get the bugs out (which is normal by the way!) I think you have a nice little machine there.

Been meaning to ask (as I'm about to do the same) - did you finish the top of the bedplate yourself on another machine or did you have it polished? I can't see machining marks or witness marks at the extremes of travel so I'm guessing you haven't leveled it using the cnc machine?